As most have said here, yes..perfectly compatible. I've had mine with autotune almost since day 1 and it's the best modification I've ever made to any bike. You'll love it!!
I would say you're probably better off having it installed if you can be assured the tech who does it has done several others and knows how to set it up correctly. I was lucky and the tech at my local Victory dealer used to work for Dynojet and did a great job. The only folks I know of that have had problems with their PCV and Autotune are the ones that installed them on their own. At least if you have it done you have some recourse if it doesn't work right on your bike.
2012 Victory High Ball
Victory Stage 1 swept pipes and performance air filter
PCV and Autotune